Minimum vis for fish analysis = 2-m
Kelp depths = 5 -m Fish depths = 5, 10 -m Inv depths = 5 -m
Visibility data for 2015 are fake. DI was bad and set at 1.0 m; other sites set at 3.0 m
## Joining, by = "taxa"
Fish depth = 5, 10
## Joining, by = "taxa"
Note: I have yellowtail here, but they are not in the multivariate stuff since we reall only saw them once.
## Joining, by = "taxa"
## Joining, by = "taxa"
Kelp depth = 5
## `summarise()` has grouped output by 'year', 'site', 'transect', 'species', 'zone', 'area'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site', 'species', 'zone', 'area'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site', 'species', 'zone'. You can override using the `.groups` argument.
## Joining, by = "site"
Ole needs to check the definitions of canopy kelp here. I took this from his code, which wasn’t finished.
## `summarise()` has grouped output by 'year', 'site', 'zone'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site'. You can override using the `.groups` argument.
Plot the big 3 species: Macro, Nero, Ptero
## `summarise()` has grouped output by 'year'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site', 'transect', 'observer', 'species', 'zone', 'area', 'taxa'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site', 'species', 'zone', 'area'. You can override using the `.groups` argument.
Ole will want to clean up the figure
## `summarise()` has grouped output by 'year', 'site', 'transect', 'observer', 'zone', 'area'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site', 'zone', 'area'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site', 'transect', 'observer', 'area', 'zone'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site', 'zone'. You can override using the `.groups` argument.
Probably worth dropping into the supplement to show that it was mostly purple urchins. Partly interesting because there is no purple urchin fishery, but there is a red one. I think.
## `summarise()` has grouped output by 'year', 'site', 'transect', 'observer', 'zone', 'area'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site', 'zone'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'taxa'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site', 'transect', 'observer', 'area', 'zone'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site', 'zone'. You can override using the `.groups` argument.
Ugly..no aliby..
## `summarise()` has grouped output by 'year', 'site', 'transect', 'observer', 'zone', 'area'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'site', 'zone'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year', 'zone'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year'. You can override using the `.groups` argument.
Not yet transformed to wide format in order to retain SD & SE info upon saving out. Transform in the Multiariate analysis rmd.
Output data files to use for multivariate ordinations.
Use these files and not raw files. Kelp and invert data have been converted to density to account for different transect lengths etc.
## `summarise()` has grouped output by 'species'. You can override using the `.groups` argument.
Note, the y-axes are very different
## `summarise()` has grouped output by 'taxa'. You can override using the `.groups` argument.
for multivariate analysis; cut and paste to that file
fish.spp = c(“OPEL”, “HEXA”, “SECA”, “SCMA” ,“SENE”, “SEME”, ‘EMBI’,‘GOBI’)
yoy.spp = c(“SECAyoy”, “SEPIyoy”, “SEMYyoy”, “SEBYTyoy”,“RYOY”)
| Species | Common name | Group | Total |
|---|---|---|---|
| Artedius harringtoni | scalyhead sculpin | COTT | 15 |
| Aulorhynchus flavidus | tubesnout | AUFL | 240 |
| bait | bait-sardines-anchovy | BAIT | 200 |
| Chirolophis nugator | mosshead warbonnet | CHNU | 3 |
| Clupeidae | herring | BAIT | 148 |
| Cottidae | sculpins | COTT | 7 |
| Embiotocidae | surfperches | EMBI | 5 |
| Embiotoca lateralis | striped surfperch | EMBI | 470 |
| Enophrys bison | buffalo sculpin | COTT | 0 |
| Hexagrammos decagrammus | kelp greenling | HEXA | 522 |
| Hemilepidotus hemilepidotus | red Irish lord | HEXA | 7 |
| Hexagrammos lagocephalus | rock greenling | HEXA | 5 |
| Hexagrammos stelleri | whitespotted greenling | HEXA | 4 |
| Jordania zonope | longfin sculpin | COTT | 4 |
| Myoxocephalus polyacanthocephalus | great sculpin | COTT | 0 |
| Ophiodon elongatus | lingcod | OPEL | 45 |
| Oxylebius pictus | painted greenling | HEXA | 7 |
| Pholididae | gunnels | PHOL | 1 |
| Rhinogobiops nicholsii | blackeye goby | GOBI | 28 |
| Rhacochilus vacca | pile perch | EMBI | 11 |
| Rimicola muscarum | kelp clingfish | RIMU | 3 |
| Sebastes yoy | rockfish yoy | RYOY | 199 |
| Scorpaenichthys marmoratus | cabezon | SCMA | 23 |
| Sebastes mela-flav yoy | yellowtail-black yoy | SEBYT | 3544 |
| Sebastes caurinus | copper rockfish | SECA | 160 |
| Sebastes flavidus | yellowtail rockfish | SEFL | 1 |
| Sebastes maliger | quillback rockfish | SEMA | 20 |
| Sebastes melanops | black rockfish | SEME | 1387 |
| Sebastes mystinus | blue rockfish | SEMY | 36 |
| Sebastes nebulosus | china rockfish | SENE | 17 |
| Sebastes pinniger | canary rockfish | SEPI | 103 |
| Synchirus gilli | manacled sculpin | COTT | 5 |
| 4008 | |||
| fish | unidentified fish | UNID | 1 |